Stereochemistry

 

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  1. two compounds
    1. two structures can have different conformations and still be considered to be equivalent because they can be rotated along sigma bonds to be equivalent (same) or super-imposable
    2. different compounds
      1. non-isomeric compounds have different atoms or number of atoms
        1. non-isomeric compounds have different properties
      2. isomers are different compounds that have the same molecular formula
        1. constitutional or structural isomers are connectivity isomers (different base name)-same atoms different connections
          1. constitutional isomers have different properties
        2. stereoisomers have the same connectivity (same base name) but different three-dimensional arrangement of atoms
          1. diastereomers are not mirror images of each other
            1. diastereomers can be chiral or achiral
            2. examples
              1. cis vs. trans
              2. E vs. Z
              3. endo vs. exo
              4. syn vs. anti
              5. r vs. s
              6. RR vs. SR
            3. diastereomers have different properties
              1. diasteromers have different physical properties
              2. diastereomers have different biological properties
          2. enantiomers are non-super-imposable (different) mirror images
            1. symmetric molecules do not have enantiomers because they contain two mirror images so when viewed in a mirror you see both mirror images again or the original object again
              1. point symmetry
              2. axis and reflection symmetry
              3. plane symmetry
            2. enantiomers are asymmetric (dissymmetric)
            3. asymmetric molecules are also called chiral like the Greek for hand
              1. symmetric molecules are also called achiral
            4. an example of a chiral molecule is a molecule with an odd number of chiral centers
              1. chiral centers are tetrahedral atoms with four different (non-isomeric, constitution, diastereomers) groups attached
                1. carbon
                2. nitrogen in aziridines but otherwise tunneling of non-bonding electrons leads to inversion of configuration easily on nitrogen
                3. sulfur (sulfone) where non-bonding electrons are given the lowest priority (Prilosec, Nexium)
              2. the configuration  (R or S) of chiral centers is assigned by the Cahn-Ingold-Prelog rules
                1. the chiral center can be represented using wedges (forward) and slashes (back)
                2. Fischer projections (bow ties on the horizontal lines)
                3. Newman projections (circle is back carbon)
                4. Haworth projections (hexagon or pentagon with vertical lines)
              3. tetrahedral atoms that have four different groups but two of the groups are mirror images of each other are not chiral centers, they are pseudo-chiral centers, assigned with little r and s.
              4. tetrahedral atoms that have four different groups that are two pairs of mirror images are chiral centers
              5. chiral centers and pseudo chiral centers are called stereogenic centers because interchanging the position of two groups on the centers (also called inversion of configuration) leads to a new stereoisomer
                1. interchanging two groups on a chiral center in a molecule with one chiral center leads to enantiomers
                2. interchanging two groups on a chiral center in a molecule with more than one chiral center leads to diastereomers called epimers (one exception)
                3. interchanging two groups on a pseudo-chiral center leads to diastereomers
            5. molecules with an even number of chiral centers (including zero) may be chiral or not
              1. allenes are examples of molecules that are chiral but do not have chiral centers
              2. spiro compounds are examples of molecules that are chiral but do not have chiral centers
              3. conformational isomers may also be chiral
                1. biphenyls
                2. binaphthyls
              4. symmetric molecules with chiral centers (R, S) are called meso
            6. enantiomers have the same properties in symmetric environments
              1. enantiomers have the same physical properties
                1. melting point, boiling point, solubility, heat of combustion, IR, NMR, etc.
            7. enantiomers have different properties in asymmetric environments
              1. enantiomers have different biological activity because biomolecules are chiral
                1. you are what you eat (cereal box chemicals)
                  1. carbohydrates are mostly D
                  2. alpha-amino acids (building blocks of proteins, enzymes) are mostly L
                  3. lipids
                    1. triglycerides
                    2. cholesterol
                2. smell
                  1. carvone
                    1. (-)-enantiomer =  (S)-2-methyl-5-(1-methylethenyl)cyclohex-2-en-1-one = mint
                    2. (+)-enantiomer = (R)-2-methyl-5-(1-methylethenyl)cyclohex-2-en-1-one = rye bread
                  2. limonene
                    1. orange smell-(+)-(R)-1-methy-4-(pro-1-en-2-yl)cyclohex-1-ene
                    2. pine smell-(-)-(S)-1-methy-4-(pro-1-en-2-yl)cyclohex-1-ene
                  3. citronellol
                    1. citronella candels-(+)-(R)-3,7-dimethyloct-8-en-1-ol
                    2. rose smell-(-)-(S)-3,7-dimethyloct-8-en-1-ol
              2. enantiomers can be differentiated by optical rotation using polarizers in a polarimeter
                1. rotation = specific rotation x concentration x path length
                2. specific rotation = rotation/(c x l)
                3. specific rotations may be over 360° as observed with low concentrations of compound
                4. (+)-dextrorotatory enantiomer, old d
                5. (-)-levorotatory enantiomer, old l
                6. ([major enantiomer]-[minor enantiomer])/([major enantiomer]+[minor enantiomer]) = enantiomeric excess = e.e., assuming only enantiomers
                7. |observed specific rotation (assuming only enantiomers)| = e.e. x rotation of pure (+)-enantiomer,
                8. e.e. = |observed specific rotation| / rotation of pure (+)-enantiomer
                9. if you make [major enantiomer] + [minor enantiomer] = 1, relative concentration
                  1. e.e. = [major enantiomer]-[minor enantiomer]
                  2. e.e.+1 = 2 x [major enantiomer]
                  3. [major enantiomer] = (e.e.+1)/2
                  4. [minor enantiomer] = 1-(e.e.+1)/2 = (1-e.e.)/2
            8. an equal mixture of enantiomers is called a racemic mixture
              1. racemic mixtures have different properties than those of pure enantiomers
                1. D, L tartaric acid (+)-(2R,3R)-2,3-dihydroxybutanedioic acid
                2. meso-tartaric acid  (2R,3S)-2,3-dihydroxybutanedioic acid
                3. racemic tartaric acid
              2. enantiomers can be separated or resolved by forming diastereomers or diastereomeric interactions
                1. for example, racemic carboxylic acids can be resolved by forming diastereomer salts with chiral amines
                2. enantiomers can be separated using chiral chromatography
              3. separation of enantiomers is big business
                1. the enatiomeric switch
                  1. Prilosec goes to Nexium
          3. a molecule with n chiral centers
            1. can have up to 2n-# meso structures = stereoisomers in its family or
            2. 2n - # meso structures -1 stereoisomers
            3. if a compound is chiral it has only one enantiomer
            4. if a compound is achiral it does not have an enantiomer
            5. if a compound is chiral it can have up to 2n-2 diasteromers

 

 

 

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Saturday, January 16, 2021 21:20